plot.q_mediation: Plot Method for the Output of 'q_mediation' Family
In manymome: Mediation, Moderation and Moderated-Mediation After Model Fitting
View source: R/q_mediation_plot.R
plot.q_mediation R Documentation
Plot Method for the Output
of 'q_mediation' Family
Description
Plot the path model
fitted by the family of 'q_mediation'
functions.
Usage
## S3 method for class 'q_mediation'
plot(
x,
standardized = FALSE,
size_variables = NULL,
size_path_labels = NULL,
nchar_variables = NULL,
nchar_path_labels = NULL,
digits = 2,
rsquares = TRUE,
sigs = TRUE,
margins = c(5, 5, 5, 5),
v_pos = c("middle", "lower", "upper"),
v_preference = c("upper", "lower"),
print_indirect = TRUE,
indirect_standardized = c("none", "stdx", "stdy", "stdxy"),
size_indirect = 1,
plot_now = TRUE,
...
)
indirect_on_plot(
q_mediation_output = NULL,
digits = 2,
size_indirect = 1,
indirect_standardized = c("none", "stdx", "stdy", "stdxy"),
margins = c(5, 5, 5, 5),
original_plot = NULL
)
Arguments
x
The output of
q_mediation(),
q_simple_mediation(),
q_serial_mediation(), and
q_parallel_mediation().
(Named x
because it is required in the naming
of arguments of the plot generic
function.)
standardized
Logical. If
TRUE, betaS in the printout of
q_mediation() family will be used
in the figure, with only numerical
variables standardized. If FALSE,
the default, then the original
(unstandardized) coefficients will
be used.
size_variables
The size of
the observed variables (the
"rectangles"), to be passed
to sizeMan of
semPlot::semPaths(). Default is
NULL and the size is determined
internally based on the number of
variables.
size_path_labels
The size of
the edge labels (parameter
estimates), to be passed to
edge.label.cex of
semPlot::semPaths(). Default is
NULL and the size is determined
internally based on the number of
variables in the plot.
nchar_variables
The number of
characters to be displayed for each
variable. To be passed to
nCharNodes of
semPlot::semPaths(). Default is
NULL, equivalent to 0 for
nCharNodes, to disable abbreviating
the variable names.
nchar_path_labels
The number
of characters to be displayed for
each label for a path. To be passed
to nCharEdges of
semPlot::semPaths(). Default is
NULL, equivalent to 0 for
nCharEdges, to disable
abbreviating the labels.
digits
The number
of digits to be printed after the
decimals. To be passed
to nDigits of
semPlot::semPaths(). Default is
2.
rsquares
Logical. If TRUE,
the default, R-squares will be
drawn instead of error variances for
mediators and outcome variables
(the y variables).
sigs
Logical. If TRUE, the
default, significance test results
will be marked by asterisks, based on
the same p-values for R-squares
displayed when printing the output of
the q_mediation() family.
margins
The margins of the plot.
A numeric vector of four values:
bottom, left, top, and right. Passed
to the mar argument of
semPlot::semPaths().
v_pos
How the mediators are to
be positioned vertically. If set to
"middle", with one x variable and
one y variable, the mediators will
tend to be placed around the
horizontal line joining x and y.
If set to "upper", they will be
placed along or above this line. If
set to "lower", they will be placed
along or below this line. Note that
this only affects the initial positions.
The positions will be further adjusted
based on the free paths in the model.
This argument is to be passed to
semptools::auto_layout_mediation().
v_preference
The preference in
shifting the mediators upward
("upper") or downward ("lower")
to avoid blocking or overlapping with
any paths in the models. It is used
only whenv_pos is "middle". If
v_pos is "lower", then
v_preference will be forced to be
"lower". If v_pos is "upper",
then v_preference will be forced to
be "upper". This argument is to be
passed to
semptools::auto_layout_mediation().
print_indirect
Logical.
Whether the indirect effect(s), and
total indirect effect if applicable,
will be printed on the plot. Default
is TRUE. Used only if plot_now
is TRUE. Confidence intervals,
if stored, will be printed, at
the level of confidence used when
doing the analysis.
indirect_standardized
If
print_indirect is TRUE, which
type of
effects are to be printed: "none"
for the unstandardized (raw) indirect
effects, "stdx" for the effects with
x standardized, "stdy" for the
effects with y standardized, and
"stdxy" for the effects with both
x and y standardized.
size_indirect
The size used
when printing the indirect effects.
The final size is determined by
multiplying the final
value size_path_labels (determined
internally if it is set to NULL)
by this value. If equal to 1, then
the size used in printing the
indirect effects should be "close"
to the size of numbers on the paths.
plot_now
If TRUE, the default,
the plot will be plotted when calling
this method.
...
For the plot method,
these are optional arguments to be
passed to semPlot::semPaths() to
generate the initial plot, before
being adjusted by
semptools::auto_layout_mediation().
q_mediation_output
The original
object used to generate the plot
(the output of the q_mediation()
family).
Indirect effects will be retrieved
from this output.
original_plot
The plot
generated by the plot method. If
supplied, a new plot will be
generated and then the indirect
effects will be printed on this new
plot. If NULL, the default, the
indirect effects will be printed on
the existing plot. Space will be
added to make room for the
indirect effects only if this
argument is set. If original_plot
is not used, make sure there is
enough room at the bottom for the
indirect effects.
Details
This method requires the
semptools and semPlot packages.
They are not installed by default.
Install them first before using the
plot method.
This method draws the path models
fitted by q_mediation(),
q_simple_mediation(),
q_serial_mediation(), and
q_parallel_mediation(), with
path coefficients and R-squares.
It will try to set positions of the
variables automatically, following
the left-to-right convention: x
variables on the left, y variables
on the right, mediators between them,
and arrows (paths) flow from left to
right. The figure should usually be
usable. If not, it can be further
modified by helper functions such as
those in semptools that can
manipulate a qgraph object. For
example, semptools::move_node()
can be used to adjust the position
of a variable in the plot.
The helper function indirect_on_plot()
adds the indirect effect
estimates (as well as confidence
intervals and p-values, if
available) to a plot. The plot method
will add these effects by default,
and so users usually do not need to
use this function.
However, if the plot needs to be modified
before being drawn, this function
can be used to add the effects
after drawing the modified plot.
Value
The plot method returns a qgraph
object generated
by semPlot::semPaths(), which is
plotted by default unless plot_now
is set to FALSE. It can be further
modified by other functions that
work on a qgraph object, such as
those from semptools.
The function indirect_on_plot()
returns the object set to
q_mediation_output
invisibly. It is called for its
side-effect.
Examples
# These examples require the package
# semptools (version 0.3.2 or above).
# CI disabled in these examples.
# Please see the help page of these functions on forming
# confidence intervals for the indirect effects.
# ===== Simple mediation
out <- q_simple_mediation(x = "x",
y = "y",
m = "m",
cov = c("c2", "c1"),
boot_ci = FALSE,
data = data_med)
plot(out)
# ===== Serial mediation
out <- q_serial_mediation(x = "x",
y = "y",
m = c("m1", "m2"),
cov = c("c2", "c1"),
boot_ci = FALSE,
data = data_serial)
plot(out)
# Standardized effects
plot(out,
standardized = TRUE,
indirect_standardized = "stdxy")
# ==== Parallel mediation
out <- q_parallel_mediation(x = "x",
y = "y",
m = c("m1", "m2"),
cov = c("c2", "c1"),
boot_ci = FALSE,
data = data_parallel)
plot(out)
plot(out,
v_pos = "lower")
plot(out,
v_pos = "upper")
# ===== A user-specified mediation model
out <- q_mediation(x = "x1",
y = "y1",
model = c("x1 -> m11 -> m2 -> y1",
"x1 -> m12 -> m2 -> y1"),
cov = c("c2", "c1"),
boot_ci = FALSE,
data = data_med_complicated)
plot(out)
manymome documentation built on Jan. 8, 2026, 9:09 a.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
View source: R/q_mediation_plot.R
| plot.q_mediation | R Documentation |
Plot Method for the Output of 'q_mediation' Family
Description
Plot the path model fitted by the family of 'q_mediation' functions.
Usage
## S3 method for class 'q_mediation'
plot(
x,
standardized = FALSE,
size_variables = NULL,
size_path_labels = NULL,
nchar_variables = NULL,
nchar_path_labels = NULL,
digits = 2,
rsquares = TRUE,
sigs = TRUE,
margins = c(5, 5, 5, 5),
v_pos = c("middle", "lower", "upper"),
v_preference = c("upper", "lower"),
print_indirect = TRUE,
indirect_standardized = c("none", "stdx", "stdy", "stdxy"),
size_indirect = 1,
plot_now = TRUE,
...
)
indirect_on_plot(
q_mediation_output = NULL,
digits = 2,
size_indirect = 1,
indirect_standardized = c("none", "stdx", "stdy", "stdxy"),
margins = c(5, 5, 5, 5),
original_plot = NULL
)
Arguments
x |
The output of
|
standardized |
Logical. If
|
size_variables |
The size of
the observed variables (the
"rectangles"), to be passed
to |
size_path_labels |
The size of
the edge labels (parameter
estimates), to be passed to
|
nchar_variables |
The number of
characters to be displayed for each
variable. To be passed to
|
nchar_path_labels |
The number
of characters to be displayed for
each label for a path. To be passed
to |
digits |
The number
of digits to be printed after the
decimals. To be passed
to |
rsquares |
Logical. If |
sigs |
Logical. If |
margins |
The margins of the plot.
A numeric vector of four values:
bottom, left, top, and right. Passed
to the |
v_pos |
How the mediators are to
be positioned vertically. If set to
|
v_preference |
The preference in
shifting the mediators upward
( |
print_indirect |
Logical.
Whether the indirect effect(s), and
total indirect effect if applicable,
will be printed on the plot. Default
is |
indirect_standardized |
If
|
size_indirect |
The size used
when printing the indirect effects.
The final size is determined by
multiplying the final
value |
plot_now |
If |
... |
For the |
q_mediation_output |
The original
object used to generate the plot
(the output of the |
original_plot |
The plot
generated by the |
Details
This method requires the
semptools and semPlot packages.
They are not installed by default.
Install them first before using the
plot method.
This method draws the path models
fitted by q_mediation(),
q_simple_mediation(),
q_serial_mediation(), and
q_parallel_mediation(), with
path coefficients and R-squares.
It will try to set positions of the
variables automatically, following
the left-to-right convention: x
variables on the left, y variables
on the right, mediators between them,
and arrows (paths) flow from left to
right. The figure should usually be
usable. If not, it can be further
modified by helper functions such as
those in semptools that can
manipulate a qgraph object. For
example, semptools::move_node()
can be used to adjust the position
of a variable in the plot.
The helper function indirect_on_plot()
adds the indirect effect
estimates (as well as confidence
intervals and p-values, if
available) to a plot. The plot method
will add these effects by default,
and so users usually do not need to
use this function.
However, if the plot needs to be modified
before being drawn, this function
can be used to add the effects
after drawing the modified plot.
Value
The plot method returns a qgraph
object generated
by semPlot::semPaths(), which is
plotted by default unless plot_now
is set to FALSE. It can be further
modified by other functions that
work on a qgraph object, such as
those from semptools.
The function indirect_on_plot()
returns the object set to
q_mediation_output
invisibly. It is called for its
side-effect.
Examples
# These examples require the package
# semptools (version 0.3.2 or above).
# CI disabled in these examples.
# Please see the help page of these functions on forming
# confidence intervals for the indirect effects.
# ===== Simple mediation
out <- q_simple_mediation(x = "x",
y = "y",
m = "m",
cov = c("c2", "c1"),
boot_ci = FALSE,
data = data_med)
plot(out)
# ===== Serial mediation
out <- q_serial_mediation(x = "x",
y = "y",
m = c("m1", "m2"),
cov = c("c2", "c1"),
boot_ci = FALSE,
data = data_serial)
plot(out)
# Standardized effects
plot(out,
standardized = TRUE,
indirect_standardized = "stdxy")
# ==== Parallel mediation
out <- q_parallel_mediation(x = "x",
y = "y",
m = c("m1", "m2"),
cov = c("c2", "c1"),
boot_ci = FALSE,
data = data_parallel)
plot(out)
plot(out,
v_pos = "lower")
plot(out,
v_pos = "upper")
# ===== A user-specified mediation model
out <- q_mediation(x = "x1",
y = "y1",
model = c("x1 -> m11 -> m2 -> y1",
"x1 -> m12 -> m2 -> y1"),
cov = c("c2", "c1"),
boot_ci = FALSE,
data = data_med_complicated)
plot(out)
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